.TH PartitionTest "1" "1 Jul 2014" "User Commands"
.SH NAME
PartitionTest \- Fast selection of best-fit models for genomic data
.SH SYNOPSIS
.B partest
\-i INPUTFILE [\fIOPTION\fR]...
.SH DESCRIPTION
.\" Add any additional description here
.PP
Selects the best-fit model of evolution for many-gene DNA or Protein data
.PP
Mandatory arguments to long options are mandatory for short options too
.TP
\fB\-c\fR, \fB\-\-config\-file\fR \fICONFIG_FILE\fR
Sets the input configuration file. Run with \fB\-\-config\-help\fR for more information
.TP
\fB\-\-config\-help\fR
Shows help about configuration files
.TP
\fB\-\-config\-template\fR
Generates a configuration file template
.TP
\fB\-d\fR, \fB\-\-data\-type\fR \fIDATA_TYPE\fR
Sets the type of the input data. DATA_TYPE: \fBnt\fR (nucleotide), \fBaa\fR (amino-acid)
.TP
\fB\-\-disable\-ckp\fR
Disables the checkpointing
.TP
\fB\-\-disable\-output\fR
Disables any file-based output. This option also disables the chackpointing
.TP
\fB\-F\fR, \fB\-\-empirical\-frequencies\fR
Includes models with empirical frequencies (+F)
.TP
\fB\-g\fR, \fB\-\-pergene\-bl\fR
Estimate per-gene branch-lengths
.TP
\fB\-\-force\-override\fR
Existent output files will be overwritten
.TP
\fB\-h\fR, \fB\-\-help\-\fR
Displays a help message
.TP
\fB\-i\fR, \fB\-\-input\-file\fR \fIINPUT_FILE\fR
Sets the input alignment file (REQUIRED)
.TP
\fB\-k\fR, \fB\-\-keep\-branches\fR
Keep branch lengths from the initial topology. This argument has no effect for initial topology different than fixed
.TP
\fB\-N\fR, \fB\-\-non\-stop\fR
Algorithms do not stop if no improvement found at one step, for avoiding local maxima
.TP
\fB\-O\fR, \fB\-\-optimize\-mode\fR \fIOPTIMIZE_MODE\fR
Sets the model optimization for the best-fit partition. OPTIMIZE_MODE: \fBfindmodel\fR (find the best-fit model for each partition), \fBgtr\fR (use only GTR model for each partition (nucleic data) or AUTO for protein data)
.TP
\fB\-p\fR, \fB\-\-num\-procs\fR \fINUMBER_OF_THREADS\fR
Number of threads for model evaluation (DEFAULT: 1)
.TP
\fB\-r\fR, \fB\-\-replicates\fR \fINUMBER_OF_REPLICATES\fR
Sets the number of replicates on Hierarchical Clustering and Random search modes
.TP
\fB\-s\fR, \fB\-\-selection\-criterion\fR \fICRITERION\fR
Sets the criterion for model selection. CRITERION: \fBbic\fR (Bayesian Information Criterion) (DEFAULT), 
\fBaic\fR (Akaike Information Criterion), \fBaicc\fR (Corrected Akaike Information Criterion),
\fBdt\fR (Decision Theory). Sample size for bic, aicc and dt criteria is the alignment length
.TP
\fB\-S\fR, \fB\-\-search\fR \fISEARCH_ALGORITHM\fR
Sets the search algorithm SEARCH_ALGORITHM: \fBgreedy\fR (greedy search algorithm),
\fBgreedyext\fR (extended greedy search algorithm),
\fBhcluster\fR (hierarchical clustering algorithm),
\fBrandom\fR (multiple step random sampling),
\fBauto\fR (auto-select algorithm (DEFAULT)),
\fBexhaustive\fR (exhaustive search)
.TP
\fB\-t\fR, \fB\-\-topology\fR \fISTARTING_TOPOLOGY\fR
Sets the starting topology for optimization. STARTING_TOPOLOGY:
\fBmp\fR (creates a maximum parsimony topology for each model optimization (DEFAULT)),
\fBml\fR (creates a maximum likelihood topology for each model optimization),
\fBfixed\fR (uses a fixed ML topology for every model optimization),
\fBuser\fR (uses a user-defined topology. Requires the "-u" argument). However, if "-u" argument is used this option is automatically set
.TP
\fB\-T\FR, \fB\-\-get\-final\-tree\fR
Conduct final ML tree optimization
.TP
\fB\-u\fR, \fB\-\-user\-tree\fR \fITREE_FILE\fR
Sets a user-defined topology. This option ignores all starting topologies different from "user-defined". The tree must be in Newick format
.TP
\fB\-v\fR, \fB\-\-version\fR
Output version information and exit
.PP
.SS "Exit status:"
.TP
0
if OK,
.TP
64
usage error,
.TP
65
error with data,
.TP
69
unavailable feature,
.TP
70
internal software error (probably a bug),
.TP
74
I/O error,
.TP
78
error in configuration.
.SH AUTHOR
Written by Diego Darriba.
.SH "REPORTING BUGS"
Report PartitionTest bugs to ddarriba@udc.es
.br
PartitionTest home page: <http://code.google.com/p/partitiontest/>
.SH COPYRIGHT
Copyright \(co 2014 Diego Darriba, Guillermo L. Taboada, Ramon Doallo and David Posada.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
.br
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
